The goal of my research has been to use x-ray crystallography to determine the structure of therapeutically relevant proteins in complex with natural substrates and products, substrate and cofactor analogs and inhibitors of enzyme action. Our lab seeks to understand the binding of these small molecules to their protein targets at a level sufficient to permit the design of potent new inhibitors which may serve as lead compounds in the development of useful drugs and the improvement of currently existing drugs. My research at UCSF has focused on two targets of structure-based drug design, HIV-1 protease and E. coli thymidylate synthase. In the context of the HIV group at UCSF, I have enjoyed close collaboration with individuals from all facets of drug discovery and development, e.g., protein chemists, enzymologists, organic chemists, and CAD scientists. A stable, non-peptide inhibitor (UCSF8) of the HIV-1 protease has been developed, and the stereochemistry of binding defined through crystallographic three-dimensional structure determination. The initial compound, haloperidol, was discovered through computational screening of the Cambridge Structural Database using a shape complementarity algorithm. The subsequent modification is a non-peptidic lateral lead which belongs to a family of compounds with well-characterized pharmacological properties. This thioketal derivative of haloperidol (UCSF8) and a halide counterion are bound within the enzyme active site in a mode distinct from that observed for peptide-based inhibitors. A variant of the protease cocrystallized with UCSF8 shows binding in the manner predicted during the initial computer based search. The structures provide the context for subsequent synthetic modifications of the inhibitor. Thymidylate synthase catalyzes the reductive methylation of deoxyuridine monophosphate (dUMP) by 5,10-methylenetetrahydrofolate (CH2THF) to form deoxythymidine monophosphate (dTMP) and dihydrofolate (H2-folate). Thymidylate synthase is essential for the biosynthesis of DNA and non-essential for the biosynthesis of RNA. This unique role makes TS an ideal candidate for the design of potent inhibitors which will serve as lead compounds in the development of anti-cancer drugs. Furthermore, structural differences between human TS and TS from certain infectious agents, such as Pneumocystis carinii which infects the lungs of AIDS patients, may be exploited to design species specific inhibitors. We have studied TS to develop a method for the rational design and improvement of potent inhibitors, and also to understand on an atomic level the kinetics and catalysis of this enzyme. Throughout these studies, I have used the program MidasPlus and the Computer Graphics Laboratory at UCSF to visualize small molecule ligands, electron density, and atomic resolution protein structures determined by x-ray crystallography.